Applied Ontology 3 (2006) 1–3
IOS Press

1

YAMATO: Yet-Another More Advanced
Top-level Ontology
Riichiro Mizoguchi a,˚ and Fumiaki Toyoshima ba Research Center for Service Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1
Asahidai, Nomi, Ishikawa 923-1292, Japan.
E-mail: mizo@jaist.ac.jp
b Graduate School of Advanced Science and Technology, Japan Advanced Institute of Science andTechnology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan.
E-mail: fumiaki.toyoshima@jaist.ac.jp
Abstract. A late-comer upper ontology YAMATO is described in this paper. YAMATO sharply distinguishes itself from other existing upper ontologies in the following respects. (1) Most importantly, YAMATO is designed with both engineering and philosophical minds. (2) YAMATO is based on a sophisticated theory of roles, given that the world is full of roles. (3) YAMATO hasa tenable theory of functions which helps to deal with artifacts effectively. (4) Information is a ‘content-bearing’ entity and it
differs significantly from the entities that philosophers have traditionally discussed. Considering into account the modern society
in which a flood of information occurs, YAMATO has a sophisticated theory of informational objects (representations). (5) Quality
and quantity are carefully organized for the sake of greater interoperability of real-world data. (6) The philosophical contribution
of YAMATO includes a theory of objects, processes, and events. Those features are illustrated with several case studies, leading
to the intensive application of YAMATO in some domains such as biomedicine and learning engineering.
Keywords: YAMATO, foundational ontology, ontological analysis, formal ontology

Introduction
Upper ontology plays a key role in enhancing ontology development by giving developers a general
guideline about how to view the target domain. There now exist several upper ontologies such as DOLCE(Borgo and Masolo, 2010), BFO (Arp, Smith and Spear, 2015), GFO (Herre, 2010), and UFO (Guizzardi
and Wagner, 2010). Despite this, a new upper ontology YAMATO (Yet Another More Advanced Top-level
Ontology) has been proposed in order to solve the theoretical and practical problems that other upper
ontologies mishandle (Mizoguchi, 2010). Although it is currently being axiomatized and is not yet fullyso, YAMATO is implemented with the ontology editor Hozo1 and in OWL.2
Each upper ontology accepts as a rationale of ontology design its own combination of ontologicalchoices (Borgo and Masolo, 2010). For example, BFO takes a realist approach (Smith and Ceusters, 2010).
Designed with both engineering and philosophical minds, YAMATO currently possesses approximately 500
classes so that it will be conceptually rich enough to help effectively to build developers domain-specificontologies. Although its structure might be criticized for being too large and complex, YAMATO causes nopractical difficulty; and its users are simply recommended to employ the higher-level categories that suit
their needs, ignoring the lower-level ones. YAMATO has the following distinguishing features:
I YAMATO accepts fundamental distinctions such as continuant vs. occurrent, independent entity vs.
dependent entity, and quality vs. quantity as well as several meta-level properties with which todefine fundamental types of entities (e.g., integrity, unity, and dissectivity). For example, an object*

Corresponding author: Riichiro Mizoguchi, Research Center for Service Science, Japan Advanced Institute of Science andTechnology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan.
1
http://www.hozo.jp/
2
The Hozo and OWL files of YAMATO are freely available for use at http://www.ei.sanken.osaka-u.ac.jp/
hozo/onto_library/upperOnto.htm.
1570-5838/06/$17.00 c 2006 – IOS Press and the authors. All rights reserved

2

R. Mizoguchi et al. / YAMATO

is elucidated as an integral, unitary, and non-dissective continuant. Used in the YAMATO hierarchy
is strict single is-a inheritance in which is-a and instance-of relations are carefully defined in termsof set membership and the notion of essential property. Within its is-a hierarchy YAMATO does notplace a role (e.g., a teacher class) under the category of an independent entity (e.g., a person class).
II To deal with engineering problems (especially interoperability of engineering data), YAMATO offersa careful treatment of properties and qualities, thereby preventing terminological confusions overthem (Mizoguchi, 2010). Roughly speaking, a quality is defined as the value-free attribute that
inheres in a particular object and a property is as a complex attribute that can be represented as apair of quality and some value.3 For instance, John’s height simplicitier is a quality (but not John’sheight of 160cm) and the attribute represented by <height, 160cm> is a property.
III Taking it that functions are at the heart of artifacts (Borgo, Fransse, Garbacz, Kitamura, Mizoguchi
and Vermass, 2014), YAMATO deals well with not only organisms but also artifacts on the basis of the
fully developed notion of function (Kitamura, Koji and Mizoguchi, 2006; Kitamura and Mizoguchi,
2013; Mizoguchi and Kitamura, 2009; Mizoguchi, 2010). Its idea of systemic function covers bothbiological and artifact functions in a single framework (Mizoguchi, Kitamura and Borgo, 2016;
Borgo, Mizoguchi and Kitamura, 2016). It strictly distinguishes behaving and functioning, sincefunction is defined as a role played by a behavior in a context. In other words, whether a behavior
can perform a function or not depends entirely on in what context it is performed. For example,
waving your hands is said to be functioning only in the case where it is performed towards persons;otherwise, it is just moving your hand (mere behavioring but not functioning).
IV YAMATO sharply distinguishes processes from events to capture the ‘unfolding’ process during a‘completed’ event (Galton and Mizoguchi, 2009). An event is to be treated as a whole which extends
in its full interval and is constituted by a process, whose occurrence models well the ‘unfoldingness’of an occurrent during the event. A sequence of events (e.g., a sequence of impulses) can form aprocess. A process is intrinsically progressive (ongoing) and hence it is ‘wholly present’ at any timeat which it exists. Therefore, a process can change but no event can.
V Given that the real world is full of roles, YAMATO develops a theory of roles which divides the traditional conception of role into a role (the object to be played) and a role-holder (the player playing
the role), thus handling the problem of a vacant role, namely a role without a player. Interpreted
from this perspective, any part of an object has some role with respect to the object as a whole
which provides a context on which the role depends. YAMATO is thus based on a principle of mutual
dependence of parts and the whole. Furthermore, it distinguishes two types of parts: a genuine partand a replaceable part. For instance, a genuine part of a bike corresponds to the front wheel and its
replaceable part to a wheel that is purchased at a bike shop. This distinction is of vital importancefor a correct way of modeling objects (Mizoguchi and Borgo, 2017).
VI To deal with informational objects in the modern world, YAMATO elaborates a theory of representation according to which a representation is composed of (representation) form and content; anda representhing thing is composed of a representation and a representation medium. Examples ofrepresentations include an algorithm, a procedure, a plan, a computer program, a musical score, anovel, a painting, data, a letter, and a sentence.
Regarding Features (I) and (IV), Section 1 explains fundamental distinctions in categories and attributes,
meta-level attributes, is-a relation, top-level categories, and the distinction between objects, processes, andevents. Section 2 presents part of the first-order formalization of YAMATO. Section 3 illustates mainly
Features (II), (IV), (V), and (VI) with several case stuides. Section 4 offers some application examples of
YAMATO , a fair number of which pertain to Feature (III).
3

The term ‘attribute’ here and henceforth is used as the most generic term for properties/qualities. Note that the term ‘essential
property’ is exceptionally employed in the paper instead of ‘essential attribute’ in conformity with its conventional usage.

R. Mizoguchi et al. / YAMATO

3

1. Principles and structures of YAMATO
1.1. Fundamental distinctions in categories and attributes
The following list includes basic distinctions in YAMATO categories and attributes:
1. Substrate vs. entity. Space and time are indispensable for the mode of existence of entities, i.e. theindividuals that are said to exist in space and time. Taking into account engineering utility, YAMATO
assumes Newtonian spacetime: three-dimensional Euclidean space and absolute time. Matter is lessfundamental to reality than, but have a close affinity with, space and time in the sense that every
physical individual is made of/from matter. Examples of matter include water and iron (represented
by the chemical formulas ‘H2 O’ and ‘Fe’, respectively).
2. Independent entity vs. dependent entity. An entity is independent if it exists independently of anything else and independent entities exist by themselves. Examples include a human, a car, and to
walk. An entity is dependent if it depends existentially on another entity and some dependent entities inhere in an object. Examples include a height, a husband, and a fragility. Typical examples ofdependent entities include qualities (e.g., a height) and dispositions (e.g., fragility).
3. Basic type vs. role. Roles are entities that depend on a context and can be played by another entity(Mizoguchi, Sunagawa, Kozaki and Kitamura, 2007). YAMATO possesses a broad classification ofroles (Mizoguchi, Galton, Kozaki and Kitamura, 2015). Some roles (e.g., a teacher) are object roles,
i.e. roles played by objects, while others (e.g., a preparation) are occurrent roles, i.e. roles playedby occurrents. Roles can be also divided into object-dependent roles (e.g., a wife) and occurrentdependent roles (e.g., a murderer). Interestingly enough, the part-whole relation and the participation relation between an object and an occurrent are interpretable in terms of the relation between arole and the context on which it depends.
4. Continuant (Object) vs. occurrent (process).4 There is a long-standing debate between the objectcentered (three-dimensionalist) view and the process-centered (four-dimensionalist) view of reality.
Taking it that neither of them succeeds, YAMATO attaches equal importance to objects and occurrents and defines an object as ‘a unity which enacts its external process’ or as ‘an interface between
its internal and external processes’ (Galton and Mizoguchi, 2009). See Section 1.4 for details.
5. Process vs. event. YAMATO sharply distinguishes between processes and events in accordance withordinary people’s differentiation between processes (e.g., "Mary is walking.") and events (e.g.,"Mary walked a mile.") in their natural language activity (Galton and Mizoguchi, 2009). A process
is ‘wholly present’ at any time at which it exists and it can change; whereas, an event is to occupy atime interval as a whole and it cannot change. See Section 1.4 for details.
6. Object and quality/property/attribute. No object can exist without having any attribute; and every
physical object exemplifies a couple of attributes (e.g., a color, a mass, and a size). At the same time,no attribute exists by itself since it needs an object as its bearer. Thus both an object and a quality/property intrinsically depend on each other and they are completely inseparable. The difference
between a property and a quality is discussed in Section 3.3 and in Mizoguchi (2010).
7. Quality vs. quantity. It is tempting to think, as is supported by some upper ontologies, that quantity
is an instance of quality because, e.g., the 15 cm length of my pencil seems to be an instance oflength (quality). YAMATO nevertheless draws a marked distinction between quality and quantity.
As a result, quantity is defined as a generically dependent continuant and, independently of quality,
quantity has its own is-a hierarchy according to which there are four subtypes of quantiy based on
Steven’s (1946) theory of scales of measurement: nominal, ordinal, interval, and ratio.
8. Physical and abstract. Independent entities fall into physical entities, semi-abstract entities, andabstract entities. A physical entity depends existentially on both space and time. Examples include
continuants and occurrents. A semi-abstract entity depends only on time (but not on space). Ex4

We mean by ‘process’ occurents in general until we discuss the difference between processes and events.

4

R. Mizoguchi et al. / YAMATO

amples include contents (e.g., propositions) and representations. An abstract entity depends neither
on space nor on time. Examples include numbers, sets, and truth-values. A non-paradigmatic but
interesting abstract entity may be a structure (e.g., a crystal structure).
9. Entity and relation. A relation holds between entities and it is something ‘higher-order’ in thisrespect. Examples of relations include friendship, a marital relation, and the part-whole relation.
Although it is intangible, a relation is not to be understood as abstract because it is time-depedent in
the sense of coming into existence at a particular time in the world. One serious issue with relations
is that formalistic thinking sometimes leads to the confusion between entities and relations. Actions
and attributes are often misconceived as relations but they are existing entities, for example, because
an action and an attribute can be formalized as a relation between an actor and an occurrent and asa relation between an object and a value, respectively.
10. Entity stacking. To address the problem of material coincidence, YAMATO adopts the entity stacking theory to allow two different entities (e.g., a vase and amount of clay) to occupy the same
spaciotemporal region (Vieu, Borgo and Masolo, 2008).
11. Informational object (representation) vs. non-informational object. As compared to non-informational
objects (e.g., objects, processes,attributes, and relations), examples of informational objects include
music, novels, texts, and symbols. Less attention has been paid to informational objects in upper ontologies in general than to non-informational objects, but YAMATO elaborates a theory of the former
since a fine-grained model of the real (especially modern) world requires an in-depth discussion ofrepresentation, e.g., on what the instances of representations are like (including a computer programand an algorithm as well as what exists on the Web) (Mizoguchi, 2004).
1.2. Meta-level attributes
YAMATO employs the following six mete-level attributes in order to define fundamental types of entities:

1. Sortal. Sortal is the most fundamental principle. Whether an entity is countable or uncountable canbe recognized by the nature of the noun that refers to that entity. For instance, the noun ‘desk’ iscountable and so is a desk; but ‘water’ is a mass noun and water is uncountable. Thus the term‘yellow thing’ fails to be accepted in YAMATO. Consider the question "How many yellow things are
there in the room?", assuming that there is exactly one yellow table in the room.
2. Identity. Identity is crucial but mysterious. For the sake of practical ontological modeling, YAMATO
exploits identity criterion of entities to determine the subsumption relation between two types ofentities, although it is extremely difficult to specify identity criteria of most entities. At a domainspecific level, for instance, a group of people fails to subsume a company because a company preserves its identity despite a change in its group-of-people identity (e.g., in its employees).
3. Integrity. An entity is integral if its parts are identifiable. Examples of non-integral entities include
10g of salt. 10g of salt preserves its identity irrespective of the replacement of any grain thereof
because reference to 10g of salt (as compared to a pile of salt which is 10g in weight on thisparticular table) does not identify which grain of salt is to belong to it.
4. Unity. An entity is unitary if the mereological sum of its parts are said to be a whole in virtue ofthe nature of those parts and the relations among them. Examples of non-unitary entities include
arbitrary aggregations of entities (e.g., an aggregation consisting of the Moon and the number 3).
5. Dissectivity. An entity is dissective if its parts fall into the same type of that of the entity. Examples
of dissective entities include a forest, a network, and a lump of butter.
6. Rigidity. A class is rigid if its instances belong to the class in virtue of their essential property (seeSection 1.3) and a class is anti-rigid if there is no essential property in virtue of which any instanceof the class belong to it. A paradigmatic example of anti-rigid classes is ‘role classes’ e.g., a student
class and a president class. Is-a relation holds only between rigid classes in YAMATO.

R. Mizoguchi et al. / YAMATO

5

Fig. 1. Top-level categories.

1.3. Is-a relation and top-level categories
Strongly influenced by Guarino’s (1995) view of upper ontology, YAMATO adopts is-a single inheritanceso that its taxonomic structure will be as simple as those of BFO and DOLCE (see Figure 1). The basic
assumption behind the set-theoretic formalization of is-a and instance-of relations in YAMATO is that each
entity has its own essential property: a property in virtue of which the entity preserves its identity.5 A set
X is a class when and only when, for every element x of X, x has an essential property in common andthis property satisfies the intension of X; and at the same time, x bears instance-of relation to (that is tosay, x is an instance of) X. Is-a relation holds between a set X and a set Y when and only when X and Y
are classes and the set of the instances of X is a subset of the set of the instances of Y .
Is-a relation in YAMATO implies inheritance of essence and an identity criterion by a certain class(X) from its superclass (Y ). Thus, is-a multiple inheritances should be avoided because no entity canhave multiple essential natures in theory. The problem of is-a multiple inheritance can be, for the mostpart, circumvented through a sharp distinction between is-a relation and role-playing relation (Mizoguchi,
Sunagawa, Kozaki and Kitamura, 2007). Consider for instance "Apple class is-a Fruit class" and "Apple
class is-a Goods class". The latter is-a relation is incorrect because goods are to be conceptualized as arole. In a domain ontology, however, the simple use of is-a single inheritance may not be useful enough toencompass domain experts’ different viewpoints on the same entity. This practical issue is to be addressedwith the application of the methodology of dynamic is-a hierarchy generation that is based on is-a single
inheritance and implemented in the Hozo ontology editor (Kozaki, Hihara and Mizoguchi, 2012).
1.4. Objects, processes and events
The conception of objects, processes, and events in YAMATO is owed to Galton and Mizoguchi (2009).
The three-dimensionalist (3D) and four-dimensionalist (4D) views of reality say that objects are prior toprocesses and that processes are prior to objects, respectively. Taking it that neither of them is plausible,
5

The work on the YAMATO set-theoretic axiomatization of is-a and instance-of relations is currently under review in a journal.

6

R. Mizoguchi et al. / YAMATO
Table 1The YAMATO categories here used.
Category

Description

Category

Description

EVNT
INTR
PROC
TIME

event
temporal interval
process
time

INST
OBJ
ROLE

temporal instantwhole object
role

YAMATO takes, so to speak, a three-and-a-half dimensionalist (3.5D) view of reality: objects and processes

are mutually dependent on each other. This worldview leads to the characterization of an object as ‘aunity which enacts its external process’ or as ‘an interface between its internal and external processes’.
For instance, a river as an object has, as its external process, changing its course of water flowing (but notwater flowing, which is its internal process).
Concerning processes and events, both kinds of occurents are temporally extended unlike objects. On
the one hand, a process is intrinsically ‘ongoing’ and it is ‘wholly present’ at any time at which it exists.
Therefore, processes are mutable and preserve their identities like objects: they can have different properties at different times. On the other hand, an event is essentially ‘completed’ and it occupies exactly anentire spacetime region.6 Events differ significantly from processes in the sense of being immutable. Each
event (e.g., a walk event) is constituted by a process (e.g., a walking process).
Further elucidation of the difference between processes and events is offered in terms of two kinds ofparts of occurrents in YAMATO: temporal parts and causal parts. A temporal part of an occurrent corresponds to a mereological part of an object. A causal part of an occurrent is the part which contributes
functionally to the occurrent. Processes and events have causal parts, whereas events (but not processes)
have temporal parts. Suppose for instance that John sneezes while he is walking. The alternate motionof John’s legs is a causal part of John’s walking process since John’s walking depends essentially on the
motion of his legs; in contrast, John’s sneezing is not a causal part of John’s walking process. Neither the
motion of John’s legs nor John’s sneezing is a temporal part of John’s walking process. In short, every
temporal part of an occurrent is a causal part of the occurrent, but not vice versa.
2. The formalization of YAMATO in first-order language
YAMATO is partially axiomatized: for instance, its process/event-related module (Borgo and Mizoguchi,2014) and its role-related module (Mizoguchi, Galton, Kozaki and Kitamura, 2015) have been formalized.
This section presents part of the former formalization. Extracted from Borgo and Mizoguchi (2014), Table 1 and Table 2 show the relevant categories and the relations among them, respectively. They are also
graphically shown in Figure 2. Future formal development of YAMATO includes to deepen the current axiomatization and to formalize the rest, e.g., regarding the categories of quality/quantity and representation
so that, ontologically and formally, YAMATO will be closely comparable to other upper ontologies.
The parthood relation P used in YAMATO has the axiomatization of Closed Extensional Mereology(CEM) (Casati and Varzi, 1999). it is binary on events and temporalized, thus ternary, on processes andobjects. The other mereological relations and operators, like O (Opx, y stands for ”x and y overlap”),
PP (PPpx, yq for “x is a proper part of y”), SUM (SUMpz, x, yq for “z is the sum of x, y”) and PROD
(PRODpz, x, yq for “z is the product of x, y”), are defined as usual in CEM (Casati and Varzi, 1999).
When P is applied to processes it is written Ppx, y, tq and reads “process x is part of process y at instantt.” The temporal parameter must be a temporal instant since in YAMATO a process can be part of another
only relatively to an instant. From these constraints and the theory of processes in YAMATO, the notion of a6
One way to delineate ongoingness of processes and completedness of events is to base them on A-series and B-series oftimes, respectively (McTaggart, 1908). This issue being included, the YAMATO overall formalization of time is currently underinvestigation.

7

R. Mizoguchi et al. / YAMATO
Table 2
Some YAMATO relations. Relations marked ˚ are defined.
Relation

Description

Relation

Description

CCNTR
ENCT
EVNTKND
KONST
PC
PRE
PROCT
O
PROD

causally contributes
enactsevent-kindconstitutes
participates inpresent at
process at timeoverlap
product

CNTX
EVNTT
IntFnPRCP
PLAY
PROCKND*HasPRC*PP*SUM

context
event spans timeprocess playing an internal rolepart ofplay
process-kind
has internal processproper part
sum

ENCT
HasPRCOBJECT

PROCESSIntRolPRC
CCNTR

CNTX
PLAY
&
HasROL

ROLE

CNTX
PLAY
&
HasROL

KONST
KONST

PLAY
&
HasROLEVENT
CNTX

Fig. 2. YAMATO structure (partial).

‘whole process’ (a process from its beginning to its end) is either understood as an event or is conceptually
incoherent.
(A1) says that P is additive on the category of objects OBJ (as usual, we assume that free variables informulas are universally quantified)(A1)

OBJpxq ^ OBJpyq ^ SUMpz, x, yq Ñ OBJpzq(additivity on OBJ)

This holds as well on events EVNT and processes PROC which are also additive. For processes, we needto introduce the binary relation ‘being present at’, written PRE, which has as second argument a time, andis itself dissective:
(A2)
(A3)
(A4)
(A5)
(A6)
(A7)

EVNTpxq ^ Ppy, xq Ñ EVNTpyq(dissectivity on EVNT)
EVNTpxq ^ EVNTpyq ^ SUMpz, x, yq Ñ EVNTpzq(additivity on EVNT)
PREpx, tq Ñ TIMEptq
PREpx, tq ^ Ppt1 , tq Ñ PREpx, t1 q
(dissectivity on PRE)
PREpx, tq ^ PROCpxq ^ Ppy, x, tq Ñ PREpy, tq ^ PROCpyq(dissectivity on PROCq
PREpx, tq ^ PROCpxq ^ PREpy, tq ^ PROCpyq ^ SUMpz, x, y, tq Ñ PREpz, tq ^ PROCpzq(additivity on PROC)

We anticipate that Ppx, y, tq, with x, y processes, holds only if t is an instant, both x, y exist at this instantt, and all the (active) participants in y are (active) participants in x.7 Furthermore, the notion of enactor,
which we can model logically as the sum of all the active participants, would suffice to define P on
processes.
7

An active participant is a participant that is relevant for the given process like the person in a walking process and the shopfloor
in a production process. This notion is not further characterized here.

8

R. Mizoguchi et al. / YAMATO

The relation of participation, PC (participates in), applies to an object and an event or process (A8);each event and process has at least one participant (A9); each object participates in some event or process(A10); a participant in an event or process is participant also in any larger event/process (A11); and any
part of an object participates in the events and processes in which the object itself participates (A12). See
also Borgo and Masolo (2009):(A8) PCpx, y, tq Ñ OBJpxq ^ pEVNTpyq _ PROCpyqq ^ TIMEptq(A9) pEVNTpxq _ PROCpxqq ^ PREpx, tq Ñ DypPCpy, x, tqq(A10) OBJpxq ^ PREpx, tq Ñ DypPCpx, y, tqq(A11) PCpx, y, tq ^ Ppy, y 1 , tq Ñ PCpx, y 1 , tq
(A12) PCpx, y, tq ^ Ppx1 , x, tq Ñ PCpx1 , y, tq
Finally, we assume that instants form a complete dense order. This is used in the formalization to model
the special relationship between events and processes. Intervals could be reconstructed from instants as
usual in knowledge representation (Tsang, 1987) but in practice here we consider both as primitives. In
particular, we assume that a time is an instant or an interval but not both (A13); an instant is a time withno proper part (A14); and an interval is a time that has a time as proper part (A15). We assume that time(intervals and instants) is modeled by the real line but this is not enforced by the axiomatization itself.
(A13)
(A14)
(A15)

TIMEptq Ñ pINSTptq _9 INTRptqq
INSTptq Ñ TIMEptq ^ @x PPpx, tq
INTRptq Ñ TIMEptq ^ Dx pTIMEpxq ^ PPpx, tqq

We write EVNTT px, tq when t is the instant or interval spanned by the event x; and PROCT px, tq when
the process x is ongoing at instant t.
(A16)
(A17)

EVNTT px, tq Ñ EVNTpxq ^ TIMEptq
PROCT px, tq Ñ PROCpxq ^ INSTptq

We will write t ă t1 for TIMEptq and TIMEpt1 q to mean that time t is (starts) earlier than time t1 . We use
the relation ă (or ď as well as their inverses) only over TIME.
3. Analysis and formalization in YAMATO: examples

3.1. Composition/constitution
1) “There is a four-legged table made of wood. Some time later, a leg of the table is replaced. Even later,
the table is demolished so it ceases to exist although the wood is still there after the demolition.”
GOAL: the example aims to show if and how the ontology models materials, objects, and components andthe relationships among them.
FOCUS: the relationship between the wood and the table and the table’s parts over time. (Artefacts andfunctions are not the focus.)
Composition and constitution of an object is explicable in terms of the role-based characterization ofparts of the object (Mizoguchi and Borgo, 2017).8 The underlying assumption is the constitution view ofobjects: except for, e.g., subatomic particles, every physical object is made of/from some amount of matter(see Section 1.1). According to the role interpretation of parthood, an entity (potential player) plays a partrole (role) with respect to an object (context), thereby becoming a part (role-holder) of the object. In thisformalization, the entity is a replaceable part because it can be substituted by another entity that is of the
8

The reader is recommended to read first Section 3.2 to understand the YAMATO theory of roles.

9

R. Mizoguchi et al. / YAMATO
Table 3Categories and relations for composition/constitution and case analysis
Notation
MAT
TIME
OBJ
ROLE
QUAL
inherepx, yq
P
SUM
ROHOpx, tq

Description
matter, material (see Section 1.1)
time (from Table 1)
object (from Table 1)role (from Table 1)quality (see Section 3.3)
x inheres in y (see Section 3.3)
part of (from Table 2)sum (from Table 2)
role-holder x is present at time t

Notation
PREpx, tq
constipx, y, tq
CNTXpx, yq
dependpx, yq
bearpx, y, tq
PLAYpx, y, tq
holdpx, y, tq

Description
present at (from Table 2)x constitutes y at trole x has y as context (from Table 2)x depends on yobject x bears quality y at t
object x plays role y at time t(from Table 2)
object x holds role y at time tsame kind; and the part of the object is a genuine part because it is spatiotemporally located exactly to thespecification of the part role under consideration.
Part of the issue of identity over time is to be addressed with a distinction between replaceable partsand genuine parts of an object. An object persists unless the specification given by part roles of the object
is violated, even if the object undergoes various changes, including the replacement of its parts (or more
precisely, of its replaceable parts). An object perishes when its specification fails to be met and the amountof matter that constitutes the object still persists after the demolition.9
Core formalization of composition and constitution (see Table 3; see also Section 3.2)
p♠q OBJpxq ^ TIMEptq ^ PREpx, tq Ñ Dy pMATpyq ^ constipy, x, tqq
ROLEpxq Ñ Dy, z pCNTXpx, yq ^ QUALpzq ^ dependpz, yq ^ inherepz, xqqp♣q PLAYpx, y, tq ^ QUALpzq ^ inherepz, yq Ñ holdpx, y, tq ^ bearpx, z, tq
p♦q Ppx, y, tq ^ OBJpyq ^ TIMEptq Ñ Dz pCNTXpz, yq ^ holdpx, z, tqqp♥q ROHOpx, tq Ø Dy pROLEpyq ^ holdpx, y, tqq
Formalization for case analysis (see Table 3)“There is a four-legged table (T1 ) made of an amount of wood (W1 ) at t1 . T1 is composed of a top-board(TB1 ) and four legs (L1 , L2 , L3 , and L4 ). TB1 is made of a board (B1 ); and L1 , L2 , L3 , and L4 are madeof four rods R1 , R2 , R3 , and R4 , respectively. At t2 , a leg L4 of the table is replaced in such a way that
L4 and T1 are made of another rod (R41 ) and another amount of wood (W2 ), respectively. The table isdemolished at t3 and it ceases
Ź to exist.” The notations T B1 R, Li R,
ŹT BP , and Li P are also introduced
so that ROLEpT B1 Rq ^ 1ďiď4 ROLEpLi Rq ^ QUALpT BP q ^ 1ďiď4 QUALpLi P q holds. Note that
T BP and Li P are semantically read as "being in an appropriate position for a top-board"and "being in an
appropriate position for Li ", respectively.
1 q ^ pPREpT1 , tq Ñ t ă t3 q ^ MATpW1 q ^ MATpW2 q ^ MATpB1 q ^ŹThe following holds: OBJpT
1 q^W “ SUMpT B , R , R , R , R q^W “ SUMpT B , R , R , R , R1 q^
MATpRq^MATpR
i
1
1
1
2
3
4
2
1
1
2
3
4
4
1ďiď4
Ź
Ź
dependpT BP, T1 q ^ 1ďiď4 dependpLi P, T1 q ^ inherepT BP, T B1 Rq ^ 1ďiď4 inherepLi P, Li Rq ^Ź
pTB1 px, tq Ø holdpx, T B1 R, tqq ^ 1ďiď4 pLi px, tq Ø holdpx, Li R, tqq.10
ŹŹ
t1 ď t ă t2 Ñ PLAYpB
Ź1 , T B1 R, tq^ 1ďiď4 PLAYpRi , Li R, tq^QUALpT BP q^ 1ďiď4 QUALpLi P q^
inherepT BP, T B1 q ^ 1ďiď4 inherepLiŹ
P, Li Rq
6
t
ď
t
ă
t
Ñ
holdpB
,
T
B
R,
tq
^
2
1
1
1ďiď4 holdpRi , Li R, tq ^ bearpB1 , T BP, tq ^
Ź 1
bearpR
,
L
P,
tq
p7
p♣qq
i
i
1ďiď4
9
It is assumed in this section that composition is restricted: composition occurs only in some appropriate situations (a full
explanation of which is beyond the scope of the present paper).
10
A rod is here treated as a kind of material (wood) for the sake of simplicity, although it is used in compounds frequently
enough to be modeled better as a role-holder which an amount of wood plays a rod role in some context, thereby becoming.

10

R. Mizoguchi et al. / YAMATO
Table 4
Categories and relations for roles and case analysis
Notation
ROLE
OBJ
TIME
QUAL
TERO
TEER
HUM
STRO
STU

Descriptionrole (from Table 1)
object (from Table 1)time (from Table 1)quality (see Section 3.3)
teacher roleteacherhuman
student role
student

Notation
CNTXpx, yq
PLAYpx, y, tq
dependpx, yq
bearpx, y, tq
holdpx, y, tq
inherepx, yq
PRE
ROHOpx, tq

Descriptionrole x has y as context (from Table 2)
object x plays role y at time t (from Table 2)x depends on yobject x bears quality y at t
object x holds role y at time t
x inheres in y (see Section 3.3)
present at (from Table 2)
role-holder x is present at t

Ź
6 t1 ď t ă t2 Ñ TB1 pB1 , tq ^ 1ďiď4 Li pRi , tq psee p♥qq ("A board and four rods (including R4 )become a top-board and legs respectively, the structutal
Ź combination of which is a table.")t1 ď t ă t2 Ñ constipW1 , T1 , tq ^ PpB
,
T
,
tq
^
1ďiď4 PpRi , T1 , tq (see p♠qp♦q)
Ź1 1
1
t2 ď t ă t3 Ñ PLAYpB1 , T B1 R, tq^ 1ďiď3 PLAYpR
i , Li R, tq^PLAYpR4 , L4 R, tq^QUALpT BP q^ŹŹ
B1 Rq ^ 1ďiď4 inherepLi P, Li Rq
1ďiď4 QUALpLi P q ^ inherepT BP, TŹ
1
6
t
ď
t
ă
t
Ñ
holdpB
,
T
B
R,
tq^
2
3
1
1
1ďiď3 holdpRi , Li R, tq^holdpR4 , L4 R, tq^bearpB1 , T BP, tq^Ź1
1ďiď3 bearpRi , Li P, tq ^ bearpR
Ź 4 , L4 P, tq p7 p♣qq 1
6 t2 ď t ă t3 Ñ TB1 pB1 , tq ^ 1ďiď3 Li pRi , tq ^ L4 pR4 , tq psee p♥qq ("A board and four rods (including R41 ) become a top-board and legs respectively, theŹ structutal combination of which is a table.")t2 ď t ă t3 Ñ constipW2 , T1 , tq ^ŹPpB1 , T1 , tq ^ 1ďiď3 PpRi , T1 , tq ^ PpR41 , T1 , tq (see p♠qp♦q)1
t ě t3 Ñ holdpB1 , T B1 R, tqŹ^ 1ďiď3 holdpRi , Li R, tq 1^ holdpR4 , L4 R, tq
6 t ě t3 Ñ PpB1 , T1 , tq ^ 1ďiď3 PpRi , T1 , tq ^ PpR4 , T1 , tq p7 p♦qq

3.2. Roles
2) “Mr. Potter is the teacher of class 2C at Shapism School and resigns at the beginning of the spring
break. After the spring break, Mrs. Bumblebee replaces Mr. Potter as the teacher of 2C. Also, student Maryleft the class at the beginning of the break and a new student, John, joins in when the break ends.”
GOAL: the example aims to show if and how the ontology models the relationships between roles, players
and organizations.
FOCUS: the change of roles/players; the vacancy of the teaching position; persistence of the class whilestudents come and go.
In YAMATO, roles are anti-rigid, dynamic, and externally grounded (Masolo et al., 2004). The core of
the YAMATO conception of roles can be summarized in the schema: "A potential player plays a role ina context, thereby becoming a role-holder." A context is one or more entities (or a mereological sum ofthem) on which a role depends, hence a role as a dependent continuant. A role is an entity to be played, apotential player is an entity that can play a role, and a potential player becomes a role-holder in playing
some role. The sharp distinction between a role and a role-holder helps to conceptualize well the change
in players (but not in roles as such) and vacant roles, i.e. roles with no player.
Core formalization of roles 11 (See Table 4)
ROLEpxq Ñ Dy, z pCNTXpx, yq ^ QUALpzq ^ dependpz, yq ^ inherepz, xqqp♣q PLAYpx, y, tq ^ QUALpzq ^ inherepz, yq Ñ holdpx, y, tq ^ bearpx, z, tq
11

See Mizoguchi, Galton, Koji and Kitamura (2015) and Borgo and Mizoguchi (2014) a fuller formalization.

R. Mizoguchi et al. / YAMATO

11p♥q ROHOpx, tq Ø Dy pROLEpyq ^ holdpx, y, tqq
Formalization for case analysis (see Table 4)“Mr. Potter (P ) has been the teacher (T1) of class 2C at Shapism School (SH) since t1 . At t2 , Mr. Potter
resigns and student (S1) Mary (M ) leaves the class. At t3 , Mrs. Bumblebee (B) replaces Mr. Potter as
the teacher of 2C and a new student (S2), John (J), joins in.” The notations TERO, STRO, SCH, HUM,
T R1 , SR1 , SR2 , T 2C, and S2C 1 are also introduced so that pTEROpxq Ñ ROLEpxqq ^ pTEROpxq ^CNTXpx, yq Ñ SCHpyqq ^ pTEROpxq ^ PLAYpy, x, tq Ñ HUMpyq ^ PREpy, tqq ^ pSTROpxq Ñ
ROLEpxqq ^ pSTROpxq ^ CNTXpx, yq Ñ SCHpyqq ^ pSTROpxq ^ PLAYpy, x, tq Ñ HUMpyq ^PREpy, tqq ^ TEROpT R1 q ^ STROpSR1 q ^ STROpSR2 q ^ QUALpT 2Cq ^ QUALpS2C 1 q holds. Notethat T 2C is semantically read as "being the teacher of 2C"; and S2C 1 is as "being a student of 2C".
The following holds: HUMpP q ^ HUMpM q ^ HUMpBq ^ HUMpJq ^ PREpP, tq ^ PREpM, tq ^PREpB, tq ^ PREpP, tq ^ SCHpSHq ^ CNTXpT R1 , SHq ^ CNTXpSR1 , SHq ^ CNTXpSR2 , SHq ^dependpT 2C, SHq ^ dependpS2C 1 , SHq ^ inherepT 2C, T R1 q ^ inherepS2C 1 , SR2 q ^ pT1px, tq Øholdpx, T R1 , tqq ^ pS1px, tq Ø holdpx, SR1 , tqq ^ pS2px, tq Ø holdpx, SR2 , tqq.
t ă t1 Ñ Dx pTEROpxq ^ CNTXpx, SHq ^ PLAYpP, x, tqq ("Mr. Potter plays no teacher role.")t1 ď t ă t2 Ñ PLAYpP, T R1 , tq ^ QUALpT 2Cq ^ inherepT 2C, T R1 q
6 t1 ď t ă t2 Ñ holdpP, T R1 , tq ^ bearpP, T 2C, tq p7 p♣qq
6 t1 ď t ă t2 Ñ T1pP, tq (see p♥q) ("Mr. Potter is the teacher of 2C.")t ě t2 Ñ holdpP, T R1 , tq ^ holdpM, SR1 , tq
6 t ě t2 Ñ T1pP, tq ^ S1pM, tq (see p♥q) ("Mr. Potter resigns and Mary leaves 2C.")t2 ď t ă t3 Ñ PREpT R1 , tq ^ Dx holdpx, T R1 , tq ("The vacant teacher role T R1 persists.")t ě t3 Ñ PLAYpM, T R1 , tq ^ QUALpT 2Cq ^ inherepT 2C, T R1 q
6 t ě t3 Ñ holdpM, T R1 , tq ^ bearpM, T 2C, tq p7 p♣qq
6 t ě t3 Ñ T1pM, tq (see p♥q) ("Mrs. Bumblebee replaces Mr. Potter as the teacher of 2C.")t ě t3 Ñ PLAYpJ, SR2 , tq ^ QUALpS2C 1 q ^ inherepS2C 1 , SR2 q
6 t ě t3 Ñ holdpJ, SR2 , tq ^ bearpJ, S2C 1 , tq p7 p♣qq
6 t ě t3 Ñ S2pJ, tq (see p♥q) ("John joins in as a student of 2C.")
Vital for persistence of an organization is the nature of roles that depend on the organization as theircontext, or technically speaking, whether those roles are functional with respect to the organization (Mizoguchi and Borgo, 2017). Consider persistence of 2C. On the one hand, student roles (SR1 and SR2 ) are
not functional with respect to Shapism School, much less 2C, because students in general are operands(the object of input and output) that merely receive education in and make no meaningful contribution toschool. The replacement of students is therefore irrelevant to persistence of 2C. On the other hand, teacher
roles (T R1 ) are functional with respect to Shapism School, let alone 2C, because teachers are typicallynecessary for their school to perform its function. Thus the change of teacher roles, if not the replacementof teacher players, may affect persistence of 2C.

3.3. Property change
3.a) “A flower is red in the summer. As time passes, the color changes. In autumn the flower is brown.”
GOAL: the example aims to show if and how the ontology models change in qualities/properties.
FOCUS: the change of the color of a flower.
Discussions of ontology of qualities/properties are complicated by significantly different usages of theterms ‘property’ and ‘quality’ in a number of different domains, including philosophy, formal logic, andcomputer science. The YAMATO theory of qualities/properties possesses two central features together with

12

R. Mizoguchi et al. / YAMATO
Table 5
Categories and relations for quality/quantity and case analysis
Notation
ROLE
TIME
DPEN
OBJ
GQT
QRT
QRHT
QUAL
QVA
QUAN
NUM
UNIT
PROP
PRE

Description [Example]
role (from Table 1)time (from Table 1)
dependent entity (see Section 1.1)
object (from Table 1)
generic quality type [length]
quality role type [height role]quality role-holder type [height (role-holder)](instance-level) quality [John’s height]
quality value [160cm, large]
quantity [160cm, 1.6m]
number [160, 1.6]
unit, dimension [centimeter(cm), meter(m)]property [<height, 160cm>, <height, large>]present at (from Table 2)

Notation
CNTXpx, yq
PLAYpx, y, tq
holdpx, y, tq
inherepx, yq
quanfypy, z, xq
qualatpx, tq
realofpx, y, tq
instofpx, yq
ocurofpx, y, tq
QRE
INTR
PROC

Description [Example]x has y as context (from Table 2)x plays y at t (from Table 2)
object x holds role y at t
(See Section 3.2)
x inheres in yy is combined with z,
thereby becoming x
x is a quality at t
x is a realization of y at t
x is an instance of yx is an occurrence of y at t
quality realization [John’s height at t]
temporal interval (from Table 1)
process (from Table 1)

its own terminology.12 First, ‘quality’ and its related terms are characterized in terms of roles as follows:"A generic quality type (potential player) plays a quality role type (role) with respect to a specific measured
object (context), thereby becoming a quality role-holder type (role-holder)." A quality generic type is themost general kind of quality and it represents basic physical parameters (e.g., length, mass, and temperature). A quality role type is a role played by a generic quality type. Examples include a height, a weight,
and a body temperature. By playing a quality role instance, a quality generic instance becomes an instanceof a quality role-holder type. A quality is the value-free kind of quality role-holder instance that inheres ina particular object. Examples include John’s height, Mary’s weight, and Suzy’s body temperature.
Second, quality is conceptually so sharply distinguished from quantity that a quality in the abovedefined sense of the term can persist irrespective of change in its quantities and Steven’s (1946) four typesof scales of measurement (nominal, ordinal, interval, and ratio) are available in the YAMATO is-a hierarchyof quantity. Being a kind of quality value (e.g., 160cm and largeness), a quantity consists of number anda unit (e.g., 160cm). Quite importantly, a qualtity is said to have a quantity only when it is realized at aparticular time. For instance, a nurse keeps track of Suzy’s body tempeature since it exists at both times
t1 and t2 ; and quality realizations at t1 and t2 of Suzy’s body temperature are occurrences of 36.5 and36.6 degrees Celsius, respectively. Finally, a property is defined as the complex kind of attribute that canbe represented as a pair of a quality and a quality value (e.g., <height, 160cm>).
Core formalization of quality and quantity (see Table 5)Note: large-case variables (e.g., ‘X’) represent universals or class-level entities; and lowercase variables(e.g., ‘x’) represent particulars or instance-level entities.
QRTpxq Ñ ROLEpxq
QRTpxq Ø Dy, z, t pGQTpyq ^ TIMEptq ^ CNTXpx, zq ^ PLAYpy, x, tqq
GQTpxq ^ QRTpyq ^ TIMEptq ^ PLAYpx, y, tq Ñ QRHTpxq ^ holdpx, y, tq
inherepx, yq Ñ DPENpxq ^ pOBJpyq _ PROCpyqq
QRHTpxq Ñ DPENpxq
QUALpxq Ø QRHTpxq ^ Dy pinherepx, yqq
QUALpxq ^ inherepx, yq ^ inherepx, zq Ñ y “ z (Non-migration of qualities)
QUANpxq Ñ QVApxq
QUANpxq Ø Dy, z pNUMpyq ^ UNITpzq ^ quanfypy, z, xqq
12

The theory of qualities/properties presented below is primarily about qualities (in the below-defined sense of the term) ofactually measured objects, but not about the results (representations) of measurement of those objects.

13

R. Mizoguchi et al. / YAMATO
Table 6
Categories and relations for process/event and case analysis
Notation
OBJ
PROC
EVNT
QUAL
realofocurofDescription
object (from Table 1)
process (from Table 1)
event (from Table 1)quality (see Case 3.a)x is a realization of y at t (see Case 3.a)x is an occurrence of y at t (see Case 3.a)Notation
ENCT
KONST
PC
PROCT
EVNTT

Description
object x enacts process y (from Table 2)
process x constitutes event y (from Table 2)participates in (from Table 2)
process at time (from Table 2)
event spans time (from Table 2)

qualatpx, tq Ñ QUALpxq ^ TIMEptq
realofpx, y, tq ^ QUALpyq Ñ qualatpx, tq ^ Dz, v, W pinherepx, zq ^ inherepy, zq ^ QRTpvq ^CNTXpv, zq ^ holdpx, v, tq ^ QRHTpW q ^ instofpx, W q ^ instofpy, W qq
realofpx, y, tq ^ realofpz, y, tq ^ x “ z (Uniquity of realizations)
QREpxq Ø Dy, t pQUALpyq ^ realofpx, y, tqq
ocurofpx, y, tq Ñ QREpxq ^ QVApyq ^ TIMEptq
ocurofpx, v, tq^ocurofpy, w, tq^inherepx, lq^inherepy, mq^v “ w Ñ QUANpvq^QUANpwq (Weakform of uniquity of quantity)
ocurofpx, v, tq ^ ocurofpy, w, tq ^ inherepx, lq ^ inherepy, mq ^ l ‰ m ^ v “ w Ñ QUANpvq ^QUANpwq (Strong form of uniquity of quantity)
PROPpx, yq Ñ QUALpxq ^ QVApyq
Formalization for case analysis (see Table 5)“A flower (F ) is red (R) in the summer (S). The color of the flower (F C) changes with the passage oftime. In the autumn (A) the flower is brown (B).” The following holds: OBJpF q^INTRpSq^INTRpAq^
QUALpF Cq ^ QVApRq ^ QVApBq ^ inherepF C, F q. (Note that, although color is to be modeled not as aquality but as a disposition to reflect a particular range of wavelength of the light, talk of color as a quality
is momentarily accepted for the sake of simplicity.)
PREpF, Sq ^ PREpF, Aq ("The flower persists: it exists both in the summer and in the autumn.")
PREpF C, Sq ^ PREpF C, Aq ("The color quality of the flower persists.")
QREpF CSq ("F CS is the realization in the summer of the color quality of the flower.")
QREpF CAq ("F CA is the realization in the autumn of the color quality of the flower.")ocurofpF CS, R, Sq ("F CS is an occurrence of redness.")
ocurofpF CA, B, Aq ("F CA is an occurrence of brownness.")3.b) “A man is walking when suddenly he starts walking faster and then breaks into a run.”
GOAL: the example aims to show if and how the ontology models change during an event.
FOCUS: the change in the speed and mode of locomotion.
Assuming that an event to be discussed in GOAL is a ‘completed’ and immutable occurrent, change
during an event is modeled upon change in the ‘ongoing’ and mutable process that constitutes the event(see Section 1.4 for details). Change in processes shows itself mainly in two ways. First, a process canhave qualities since it is ‘wholly present’ at any time at which it is ongoing. This enables talk of ‘qualitychange’ in the realm of occurrents as well as in that of occurrents (compare: the color change of a flower
discussed in Case 3.a). Second, since a process changes and no event does, change in the ‘aspect’ or‘mode’ of an event is explicable in terms of the change involved in the process that constitutes the event.

14

R. Mizoguchi et al. / YAMATO

Core formalization of process and event 13 (see Table 6)
p5q ENCTpx, yq ^ KONSTpy, zq ^ PROCT py, tq Ñ PCpx, z, tq
Formalization for case analysis (see Table 6)“A man (O) is walking (Wp ) and walks at steady speed (S) from t0 until t1 , when O starts walking fasterand walks at an increasing speed until t2 . In short, O walks (We ) from t0 until t2 . At t2 , O breaks (Be )into a run, is running (Rp ), and runs (Re ) from t2 until t3 . Seen from a wider perspective, O is moving(Mp ) and moves (Me ) from t0 until t3 .” The following holds: OBJpOq ^ QUALpSq ^ PROCpWp q ^PROCpRp q ^ PROCpMp q ^ EVNTpWe q ^ EVNTpBe q ^ EVNTpRe q ^ EVNTpMe q ^ ENCTpO, Wp q ^ENCTpO, Rp q ^ ENCTpO, Mp q ^ KONSTpWp , We q ^ KONSTpRp , Re q ^ KONSTpMp , Me q.
t0 ă t ď t2 Ñ PROCT pWp , tq 6 t0 ă t ď t2 Ñ PCpO, We , tqp7 p5qq
t0 ă tx ď ty ď t1 ^ realofpStx , S, tx q ^ realofpSty , S, tx q ^ ocurofpStx , Sx, tx q ^ ocurofpSty , Sy, ty q Ñ
Sx “ Sy ("The man O walks at steady speed from from t0 until t1 .")t1 ă tx ď ty ď t2 ^ realofpStx , S, tx q ^ realofpSty , S, tx q ^ ocurofpStx , Sx, tx q ^ ocurofpSty , Sy, ty q Ñ
Sx ď Sy ("The man O walks at an increasing speed from t1 until t2 .")t0 ď t ď t2 Ñ EVNTT pWe , tq ^ PCpO, We , tq
t “ t2 Ñ EVNTT pBe , tq ^ PCpO, Be , tq
t2 ă t ă t3 Ñ PROCT pRp , tq 6 t2 ă t ă t3 Ñ PCpO, Re , tqp7 p5qq
t2 ď t ď t3 Ñ EVNTT pRe , tq ^ PCpO, Re , tq
t0 ă t ă t3 Ñ PROCT pMp , tq 6 t0 ă t ă t3 Ñ PCpO, Me , tqp7 p5qq
t0 ď t ď t3 Ñ EVNTT pMe , tq ^ PCpO, Me , tq
Consider the change in the mode of O’s locomotive activity, which is to be examined from either the
event (Me ) or the process (Mp ) viewpoint. O’s moving process is mutable and its walking and running
sub-processes share the nature of mobility or locomotivity with each other. By comparison, O’s movement
event is immutable and its walk and run sub-events have nothing in common because they are just temporalparts of the movement event. The change in the mode of O’s locomotion is explainable in terms of thewalking and running aspects of his moving process.
3.4. Event change
4) “A man is walking to the station, but before he gets there, he turns around and goes home.”
GOAL: the example aims to show if and how the ontology models change in goal-directed activities.
FOCUS: an activity/event is not completed and another activity/event is completed instead.
Change in goal-directed activities in general is modeled upon a complex interrelationship among theexecutions (whether completed or not) of plans, processes, and events.14 Activities are described either asprocesses or as events. While actions are classified in YAMATO as processes, activities with goal accomplishment are well modeled as events because goal-directedness of an occurrent needs its completion. In
addition, goal-directedness, completion, and incompletion of an activity is to be captured in terms of thespecification nature of a plan (to be detailed below), the execution of the plan, and the abandonment (andthus the uncompleted execution) of the plan, respectively.
A plan is interpretable from the viewpoint of the YAMATO notion of representation.15 For the discussion
to be manageable, a plan is here conceptualized as a representation whose content is a specification of
the ordering of actions to be made and whose (representation) form is a sequence of identifiers of those13

See Borgo and Mizoguchi (2014) for a fuller formalization.
A detailed study of goal-directed activities requires robust ontology of action as well as ontology of mind (e.g., the beliefdesire-intention (BDI) model of agency), which are outside the scope of the current investigation.
15
The reader is recommended to read through Section 3.5 to understand an overview of the YAMATO theory of representation.
14

15

R. Mizoguchi et al. / YAMATO
Table 7
Categories and relations for plans and case analysis
Notation
OBJ
PROC
EVNT
PLAN
REPR
ACT
SPEC
refoofpx, yq
SPAD
PLAC
ID
plcomppx, tq
TIME

Description
object (from Table 1)
process (from Table 1)
event (from Table 1)
plan
representation
actionspecification
x is a representation form of ysequence of planned actions ID
planned action
IDplan x is completed at ttime (from Table 1)

Notation
ENCT
KONST
PC
PROCT
EVNTT
P
contofpx, yq
denotepx, yq
plpartpx, yq
plexecpx, yq
complipx, yq
plabanpx, tq

Description
object x enacts process y (from Table 2)
process x constitutes event y (from Table 2)participates in (from Table 2)
process at time (from Table 2)
event spans time (from Table 2)part of (from Table 2)
x is a content of yx denotes y
x is a plan part of yx is a plan execution of yx is compliant with yplan x is abandoed at t

actions.16 A plan is executed when its content is realized, namely when a planned action (or a sequenceof planned actions) is taken. A plan is abandoned when its content is no longer realized, namely when not
all of the planned actions are taken.
A configuration of those concepts is to be used for analyzing goal-directed activities and their change.
A goal-directed process is an action that is a realization of the content (specification) of a plan. It constitutes an event with goal accomplishment when the plan is completed (fully executed). When the plan
is abandoned, however, the action process constitutes an event with the goal unachieved. What follows
this is the situation in which either the action process persists and constitutes another event; or the action
process fails to persist, another action process occurs, and it constitutes yet another event.
Core formalization of plans (see Table 7)
PLANpxq Ñ REPRpxq
ACTpxq Ñ PROCpxq
contofpx, yq ^ PLANpyq Ñ SPECpxq
refoofpx, yq ^ PLANpyq Ñ SPADpxq
plpartpx, yq Ñ PLACpxq ^ PLANpyq ^ Dw, z pIDpwq ^ refoofpz, yq ^ Ppw, zq ^ denotepw, xqq
plexecpx, y, tq Ñ ACTpxq ^ TIMEptq ^ Dw, z pcontofpz, wq ^ plpartpy, wq ^ complipx, zqq
p5q plcomppx, tc q Ñ @z Dy, s, t pt ď tc Ñ pSPECpsq ^ plpartpz, xq ^ plexecpy, z, tq ^ complipy, sq ^contofps, xqqq
p7q plabanpx, t0 q Ñ @t ě t0 Dz Dy pplpartpz, xq ^ plexecpy, z, tqqq
Formalization for case analysis (see Table 7)“A man (O) is walking (Wp ) with a plan (P ) in mind to walk to the station and he walks (We1 ) halfway
from t0 until t1 . At t1 , he turns around (Te ) and walks (We2 ) home from t1 until t2 . At t2 , he arrives (Ae ) home.”17 The notation Wplan is also introduced so that plpartpWplan , P q holds. The following
holds: OBJpOq ^ PROCpWp q ^ EVNTpWe1 q ^ EVNTpTe q ^ EVNTpWe2 q ^ EVNTpAe q ^ PLANpP q ^ENCTpO, Wp q ^ KONSTpWp , We1 q ^ KONSTpWp , We2 q ^ plexecpWp , Wplan q.
t0 ă t ď t1 Ñ PROCT pWp , tq
t “ t1 Ñ plabanpP, tq ^ EVNTT pTe , tq ^ PCpO, Te , tq (see p7q)
16
Two remarks. First, see Section 3.5 for details on a specification. Second, a sequence of identifiers do not need to be describedin natural language (e.g., in words). It is introduced here to identify the ordering of planned actions for the sake of a simple
exposition of a representation form of a plan.
17
The man’s ad hoc plan to walk back home lies outside the scope of the investigation.

16

R. Mizoguchi et al. / YAMATO

t0 ď t ď t1 Ñ EVNTT pWe1 , tq ^ PCpO, We1 , tq
t1 ă t ď t2 Ñ PROCT pWp , tq
t “ t2 Ñ EVNTT pAe , tq ^ PCpO, Ae , tq
t1 ď t ď t2 Ñ EVNTT pWe2 , tq ^ PCpO, We2 , tq
t0 ď t ď t2 Ñ plcomppP, tq (see p5q)
Consider change in O’s locomotive activity with the eventually unaccomplished goal of walking to thestation, which is to be considered from either the process or the event perspective. O’s walking process
persists throughout, regardless of whether it is a realization of the content of his initial plan to walk to thestation or not. In contrast, O’s plan change causes the occurrence of the event with the plan incomplete,the event of his turning around, and the event of his walking back home. The change in O’s entire activity
is analyzed in terms of change in his walking process that constitutes three different events.
3.5. Concept evolution
Background: a marriage is a contract between two people that is present in most social and cultural systems and it can change in major (e.g. gender constraints) and minor (e.g. marriage breaking procedures)
aspects.
5) “A marriage is a contract that is regulated by civil and social constraints. These constraints can change
but the meaning of marriage continues over time.”
GOAL: the example aims to show if and how the ontology models the evolution of the meaning of a term.
FOCUS: the continuity/discontinuity of the meaning of marriage in the presence of changing qualifications.
Since the meaning of a term is its semantic content, close examination of the evolution of the meaningof a term is based on the complex but fairly sophisticated YAMATO theory of representation in which a
representation as a ‘content-bearing entity’ is rigorously analyzed. The central idea is that a representation consists of a (representation) form and the content that depends on the representation form; and a
representing thing is composed of a representation and a representation medium. For instance, a musicalscore (representation) consists of a sequence of musical notes (representation form) and a piece of music(content); and a music book (representing thing) is composed of some musical scores (representations)and some pieces of paper (representation media).
Characteristic of a representation is that both its form and content can be repeatedly realized. The formof a representation is realized on a physical continuant: e.g., a sequence of mucial notes is realized when
it is written on a piece of paper. The content of a representation is realized by some process (typicallyby an action) when it is a specification. A specification is intuitively understood as a detailed descriptionof how something is, or should be, designed or made. Examples of representations whose content is a
specification include an algorithm and a recipe as well as a plan (discussed in Section 3.4). For instance, a
piece of music is realized when somebody plays it.
In addition, some representation forms can have the different kind of content from that of representations. To illustrate this, consider Williams Shakespeare’s Hamlet as a representation whose content is the
tragic story about the Prince of Denmark, his father’s ghost, and other characters. The representation formof Hamlet is a series of English sentences (including “To be or not to be: that is the question”) which inturn have as content Shakespeare’s wording and style of writing. In this way, a representation form has aspart non-propositional content, unlike the typically propositional content of its representation.
Quite importantly, letters are ontologized but with further complications. Consider for instance the letter
representation A that is composed of the letter representation form A and the letter content A. A means a
trajectory of a linear drawing of ‘A’. In this respect, A is ‘non-migratable’: there is uniquely A for morethan one As. The nature of A is such that A meets a standard letter figure A as a specification and A
denotes a symbol A. Both A and A are contentful. A prescribes that A must be such that two slanting sides

17

R. Mizoguchi et al. / YAMATO
Table 8Categories and relations for representation and case analysis
Notation
SEAB
OBJ
REPR
REFO
CON
RETH
REME
SPEC
TERM

Description
semi-abstract (see Section 3.1)
object (from Table 1)
representation
representation form
content
representing thing
representation medium
specification
term

NotationPPREdependpx, yq
realofpx, y, tq
PROCTdenotepx, y, tq
NAME
MEAN

Description
part of (from Table 2)
present at (from Table 2)x depends on yx is a realization of y at t
process at time (from Table 2)x denotes y at t
namemeaningof a triangle is crossed in the middle by a horizontal bar. A means the first letter of the Latin alphabet.
Moreover, a letter representing thing A has A as part. Letters are ontologically multifaceted, as shown by
the observation that the letter ‘A’ is used to refer to any of them: A , A, A, A, A, and A.
Seen from this perspective, a term is the kind of representation whose representation form is a sequenceof letters and that denotes the entity (denotation) to which the term essentially refers.18 The supposed
discontinuity of the meaning of a term is modeled as change in the content of the term because its denotation is unvarying. The term ‘marriage’ is the representation whose form is a sequence of alphabet letters(m-a-r-r-i-a-g-e) and that denotes (the nature of) marriage: the socio-legal union between two adults thatis verified by the contract between them. When marriage qualifications change, the term ‘marriage’ wouldchange at its content level while preserving its denotation.
Core formalization of representation19 (See Table 8)
Note: a representation, and its form, and its content are semi-abstract, whereas a representing thing
and its representing medium are objects. That is to say, pREPRpxq Ñ SEABpxqq ^ pREFOpxq ÑSEABpxqq ^ pCONpxq Ñ SEABpxqq ^ pRETHpxq Ñ OBJpxqq ^ pREMEpxq Ñ OBJpxqq holds.
REPRpxq Ñ Dy, z, t pREFOpyq ^ CONpzq ^ Ppy, x, tq ^ Ppz, x, tq ^ dependpz, yqq
REFOpxq Ñ Dy pCONpyq ^ dependpy, xqq
pREFOpxq ^ CONpyq ^ REFOpzq ^ CONpwq ^ dependpy, xq ^ dependpw, zq ^ y ‰ wq Ñ x ‰ z
RETHpxq Ñ Dy, z, t pREPRpyq ^ REMEpzq ^ Ppy, x, tq ^ Ppz, x, tqq
REFOpxq ^ realofpy, x, tq Ñ OBJpyq ^ PREpy, tq
REPRpxq ^ CONpyq ^ Ppy, x, tq ^ realofpz, y, tq Ñ SPECpyq ^ PROCT pz, tq
Formalization of a term as a representation (See Table 8)
TERMpxq Ñ REPRpxq
TERMpxq ^ REFOpyq ^ Ppy, x, tq Ñ NAMEpyq ^ PREpy, tq ("The form of a term is its name.")
TERMpxq ^ CONpyq ^ Ppy, x, tq Ñ MEANpyq ^ PREpy, tq ("The content of a term is its meaning.")
TERMpxq Ñ Dy pdenotepx, yq ^ @z pdenotepx, zq ^ y “ zqq ("Each term denotes exactly one entity.")(Note that the denote predicate is time-invariant: the denotation of a term is unvarying.)
Dx, y, z, t, t1 pTERMpxq ^ NAMEpyq ^ NAMEpzq ^ Ppy, x, tq ^ Ppz, x, t1 qq("The name of a term is changeable: a term can have different names at different times.")Dx, y, z, t, t1 pTERMpxq ^ MEANpyq ^ MEANpzq ^ Ppy, x, tq ^ Ppz, x, t1 qq("The meaning of a term is changeable: a term can have different meanings at different times.")18
19

Compare this with Peirce’s (1977) Semiotic.
Ontology of letters is outside the scope of the present axiomatization.

18

R. Mizoguchi et al. / YAMATO

Formalization for case analysis (See Table 8)“The term ‘marriage’ (Tm ) persists from t0 . At t1 , the meaning (M 1m ) of Tm changes into another meaning (M 2m ) in virtue of change in socio-legal constraints on marriage (whether major or minor). Tm still
persists afterwards.” The notation Dm is also introduced so that denotepTm , Dm q holds. The following
holds: TERMpTm q ^ MEANpM 1m q ^ MEANpM 2m q.
t ě t0 Ñ PREpTm , tq ("The term ‘marriage’ persists regardless of change in its meaning.")t0 ď t ă t1 Ñ PpM 1m , Tm , tq ("The meaning of the term ‘marriage’ is M 1m .")t ě t1 Ñ PpM 2m , Tm , tq ("The meaning of the term ‘marriage’ is M 2m .")The evolution of concepts (in the broad sense of the term) could be modeled upon the framework within
which a concept is the content of some representation and, when concept change occurs, the representation changes at its conceptual level while maintaining its denotation. Consider for instance the fact that,generally speaking, Japan employed as a diagnosis criterion of hypertension the value 160/95 mmHg in
1990, but it uses the value 140/90 mmHg in 2017. Understood as a kind of representation, the Japanesediagnostic criterion of hypertension has as content 160/95 mmHg in 1990 and 140/90 mmHg in 2017; andthe diagnostic criterion consistently denotes hypertension: a clinically abnormal high blood pressure.
Scientific hypotheses and their rejection might be analyzable as well in terms of the representational
interpretation of concept evolution. For example, combusion was explained by the ‘phlogiston theory’in which an unobservable substance called ‘phlogiston’ escapes from things when they burn, until thelate eighteenth century, in which Lavoisier hypothesized that a different unobservable substance which
he terms ‘oxygen’ is incorporated by things when they burn. Lavosier’s ‘oxygen theory’ is currently confirmed by atomic physics.20 Both the phlogiston theory and the oxygen theory are to be interpreted as
representations whose contents are the existence of phlogiston and oxygen, respectively; and both entities are postulated to explain the object of the scientific investigation under consideration: combustion, or
the process of burning. With the progress of science, the scientific hypothesis on combustion changes its
content from phlogiston to oxygen while having combustion as denotation.

4. Ontology usage and community impact
Several application examples of YAMATO are found in biomedicine. First of all, a viable definition of
disease is indispensable for the robust construction of disease ontologies. Built in compliace with the
YAMATO conception of objects discussed in Section 1.4, the River Flow Model (RFM) of diseases was intially presented in Mizoguchi, Kozaki, Kou, Yamagata, Imai, Waki and Ohe (2011) and further developedin Rovetto and Mizoguchi (2015) and Toyoshima, Mizoguchi and Ikeda (2017).21 The basic tenet of RFM
is the analogy between a river and a disease. Just as a river enacts changing the course of water flowing as
its external process, a disease enacts as its external process a process of, e.g., spreading and disappearing;and just as a river has water flowing as its internal process, a disease has as its internal process a numberof causal chains of clinically abnormal states. In RFM, a disease is thus defined as a dependent continuant constituted of causal chains of abnormal states. RFM is theoretically comparable to, and can be ofhigher practical value than, the widely employed, dispositional model of disease given by the Ontology
for General Medical Science (OGMS) (Scheuermann, Ceuster and Smith, 2009).
Second, and relatedly, diverse representations of abnormal states render exchanging medical data andinformation rather difficult. To address this issue, a unified representation model of abnormal states was
proposed in accordance with the YAMATO theory of quality and quantity discussed in Section 3.3 (Yamagata, Kozaki, Imai, Ohe and Mizoguchi, 2014). An abnormal state is there described as a ‘property’, which
can be decomposed into an ‘attribute’ and a ‘value’ in a qualitative representation, hence the ăEntity,
20
21

See Kitcher (1978) for a detailed theoretical discussion on phlogiston and oxygen.
http://rfm.hozo.jp/

R. Mizoguchi et al. / YAMATO

19

Attribute, Valueą formalism. This model was extensively exploited in order to capture all causal relations
among approximately 21,000 abnormal states from approximatelty 6,000 diseases.
Third, it was found on closer examination that, despite its widespread use as a common framework
for representing genomic phenotypes, the Phenotypic Quality Ontology (PATO) has some problems witha qualitative representation owing to its use of the poorly expressive ăEntity, Propertyą representation
form. To solve them, PATO was enhanced by the YAMATO qualitative representation and expanded into
PATO2YAMATO (Masuya et al., 2011).22 This indicates an effective way of integrating biological mesurement data across various biological experiments.
Fourth, and finally, genes are fundamental to modern biomedical science. Certainly, Gene Ontology
seeks to provide cross-species biological vocabularies that can be used by multiple databases to describe
gene products (Gene Ontology Consortium, 2001).23 No attempt had been nonetheless made to represent
fully various complex aspects of genes until Genetics Ontology (GXO) was constructed to provide a soundfoundation for a semantic model that is applicable to various fields of life science (Masuya and Mizoguchi,2012).24 In GXO, the multiple facets of bearers of genetic information (including genes and alleles) areaccurately modeled with the help of the YAMATO theory of roles and representation. Included in GXO is,e.g., the world’s first ontological definition of DNA as the representing thing that is encoded by adenine(A), cytosine (C), guanine (G), and thymine (T).
Other application examples of YAMATO include increased usage of the method of function decomposition (Kitamura and Mizoguchi, 2003) according to which approximately 90 functional terms can usedbe as a common vocabulary for representing a functional structure of any aritifact and that was elaborated in conformity with the YAMATO notion of function (see Feature (III) in Introduction). The approachof function decomposition was well-advanced enough to be merchandized as a tool called "OntoloGear"
which has been deployed in industry, e.g., to facilitate production systems in a factory. Moreover, the ideaof function decomposition was developed by the conception of actions as processes (rather than events)
into the method of action decomposition that enables the modeling of any complex action in terms ofapproximately 500 basic action terms. The technique of action decomposition is available in an expanded
version of OntoloGear: OntoGearCore.
The action decomposition method has been extensively employed in various domains. Examples include the modeling of nursing actions in hospitals (Nishimura, Kitamura, Sasajima and Mizoguchi, 2013);
the development of an Ontology-based Obstacle, Prevention and Solution (OOPS) modeling framework
which supports descriptions of activities and related knowledge of the users of mobile Internet services(Sasajima, Kitamura, Naganuma, Fujii, Kurakake and Mizoguchi, 2008); and the building of an ontologyof learning and instructional theories that is called ‘OMNIBUS’ (Mizoguchi and Bourdeau, 2000; Hayashi,
Bourdeau and Mizoguchi, 2009; Mizoguchi and Bourdeau, 2016) and an OMNIBUS-based theory-aware
authoring tool named ‘SMARTIES’ that provides a modeling environment and guidelines for making
theory-compliant learning and instructional scenarios (Mizoguchi, Hayashi and Bourdeau, 2007).
Other applications of YAMATO include the proposal of an ontological definition of services based on
the YAMATO theory of function (Sumita, Kitamura, Sasajima and Mizoguchi, 2012). Projects in progress
to apply YAMATO include (1) Structuring sustainable lifestyles in future society; (2) Reorganization of
the grammar of English tense; (3) Task ontology building of demolition tasks of a nuclear power plant;(3) Ontology building of biomimetics; and (4) Building a know-how model of an expert of ferromagnetic
materials. The YAMATO concepts mainly used in the project (2) and others are the process/event distinction
and the method of function/action decomposition, respectively.
22

http://ja.brc.riken.jp/lab/bpmp/ontology/ontology_pato2yato.html
http://www.geneontology.org/
24
http://ja.brc.riken.jp/lab/bpmp/ontology/ontology_gxo.html
23

20

R. Mizoguchi et al. / YAMATO

Acknowledgements
I would like to express my sincere thanks to Stefano Borgo, Antony Galton, Yoshinobu Kitamura, andKouji Kozaki for their fruitful collaboration.

References
Arp, R., Smith, B. and Spear, A. D. (2015). Building Ontologies with Basic Formal Ontology, MIT Press.
Borgo, S., Franssen, M., Garbacz, P., Kitamura, Y., Mizoguchi, R. and Vermaas, P. E. (2014). Technical artifacts: An integrated
perspective, Applied Ontology 9 (3–4), 217–235.
Borgo, S. and Masolo, C. (2010.) Ontological Foundations of DOLCE. In R. Poli, M. Healy and A. Kameas (eds.), Theory andApplications of Ontology: Computer Applications (pp. 279–295), Springer.
Borgo, S. and Mizoguchi R. (2014). A First-order Formalization of Event, Object, Process and Role in YAMATO, In P. Garbacz
and O. Kutz (eds.), Proceedings of the 8th International Conference on Formal Ontology in Information Systems (FOIS2014),
Rio de Janeiro, Brazil, September 22-26, 2014, 79–92.
Borgo, S., Mizoguchi, R. and Kitamura, Y. (2016). Formalizing and Adapting a General Function Module for Foundational
Ontologies. In R. Ferrario and W. Kuhn (eds), Proceedings of the 9th International Conference on Formal Ontology inInformation Systems (FOIS2016), Annecy, France, July 6-9, 2016, 241–254.
Casati, R. and Varzi, A. C. (1999). Parts and Places, MIT Press.
Galton, A. and Mizoguchi, R. (2009). The water falls but the waterfall does not fall — New perspectives on objects, processes
and events, Applied Ontology 4(2), 71–108.
Gene Ontology Consortium. (2001). Creating the Gene Ontology Resource: Design and Implementation, Genome Research, 11,1425–1433.
Guarino, N. (1995). Formal Ontology, Conceptual Analysis and Knowledge Representation, International Journal of Human andComputer Studies, 43(5/6), 625–640.
Guizzardi, G. and Wagner, G. (2010). Using the Unified Foundational Ontology (UFO) as a Foundation for General Conceptual
Modeling Languages. In R. Poli, M. J. Healy and A. D. Kameas (eds.), Theory and Application of Ontology: Computer
Applications (pp. 175–196), Springer.
Hayasi, Y., Bourdeau, J. and Mizoguchi, R. (2009). Strategy-centered Modeling for Better Understanding of Learning/Instructional Theories, International Journal of Knowledge and web Intelligence, 1(3–4), 187–208.
Herre, H. (2010). General Formal Ontology (GFO): A foundational ontology for conceptual modelling. In R. Poli, M. J. Healy
and A. D. Kameas (eds.), Theory and Application of Ontology: Computer Applications (pp. 297–345), Springer.
Kitamura, Y., Koji, Y. and Mizoguchi, R. (2006). An Ontological Model of Device Function: Industrial Deployment and Lessons
Learned, Applied Ontology (Special issue on “Formal Ontology Meets Industry”), 1(3–4), 237–262.
Kitamura, Y. and Mizoguchi, R. (2003). Organizing Knowledge about Functional Decomposition, In Proceedings of the 14th
International Conference on Engineering Design (ICED03), Stockholm, Sweden, August 19–21, 2003.
Kitamura, Y. and Mizoguchi, R. (2013). Characterizing functions based on phase-and evolution-oriented models, Applied Ontology 8(2), 73–94.
Kitcher, P. (1978). Theories, Theorists and Theoretical Change. Philosophical Review 87(4): 519–547.
Kozaki, K., Hihara, K., and Mizoguchi, R. (2012). Dynamic Is-a Hierarchy Generation System Based on User’s Viewpoint.
In Proceedings Joint International Semantic Technology Conference (JIST2011), Hangzhou, China, December 4–7, 2011.
096-111.
Masolo, C., Vieu, L., Bottazzi, E., Catenacci, C., Ferrario, R., Gangemi, A. and Guarino, N. (2004). Social Roles and Their
Descriptions. In D. Dubois, C. Welty and M. A. Williams (eds.), Principles of Knowledge Representation and Reasoning,
Proceedings of the Ninth International Conference (KR 2004), Whistler British Columbia, Canada, June 2-5, 2004.
Masuya, H. et al. (2011). An Advanced Strategy for Integration of Biological Measurement Data. In Proceedings of the 2nd
International Conference on Biomedical Ontology (ICBO2011), Buffalo, NY, USA, July 28–30, 2011, 79–86.
Masuya, H. and Mizoguchi, R. (2012). An Ontology of Gene. In Proceedings of the 3rd International Conference on Biomedical
Ontology (ICBO2012), Graz, Austria, July 21–25, 2012.
McTaggart, J. M. E. (1908). The Unreality of Time. Mind 17: 457-474.
Mizoguchi, R. (2004). Tutorial on ontological engineering - Part 3: Advanced course of ontological engineering, New Generation
Computing, 22(2), 198–220.
Mizoguchi, R. (2010). YAMATO: yet another more advanced top-level ontology. In Proceedings of the Sixth Australasian Ontology Workshop (pp. 1–16), Adelaide: Australia.
Mizoguchi, R. and Borgo, S. (2017). A Preliminary Study of Functional Parts as Roles. In Proceedings of the 2nd Workshop on
Foundational Ontology (FOUSTII), co-located with the 3rd Joint Ontology Workshop (JOWO2017), Bozen-Bolzano, Italy,
September 21-23, 2017.
Mizoguchi, R. and Bourdeau, J. (2000). Ontological Engineering to Overcome AI-ED Problems, International Journal of Artificial Intelligence in Education, 11(2), 107–121.
Mizoguchi, R. and Bourdeau, J. (2016). Using Ontological Engineering to Overcome AI-ED Problems: Contribution, Impact andPerspectives, International Journal of Artificial Intelligence in Education, 26(1), 91–106.
Mizoguchi, R., Galton, A., Kozaki, K. and Kitamura, Y. (2015). Families of roles: A new theory of occurrent-dependent roles,
Applied Ontology 10(3-4), 367–399.

R. Mizoguchi et al. / YAMATO

21

Mizoguchi, R., Hayashi, Y. and Bourdeau, J. (2007). Inside Theory-Aware and Standards-Compliant Authoring System, In Proceedings of the Fifth International Workshop on Ontologies and Semantic Web for E-Learning (SWEL2007), Marina del Rey,
CA, USA, July 9, 2007, 1–18.
Mizoguchi, R. and Kitamura, Y. (2009). A Functional Ontology of Artifacts, The Monist 92(3), 387–402.
Mizoguchi, R., Kitamura, Y. and Borgo, S. (2016). A unifying definition for artifact and biological functions, Applied Ontology
11(2), 129–154.
Mizoguchi, R., Kozaki, K., Kou, H., Yamagata, Y., Imai, T., Waki, K. and Ohe, K. (2011). River Flow Model of Diseases. In
Proceedings of 2nd International Conference on Biomedical Ontology (ICBO2011), Buffalo, NY, USA, July 28–30, 2011,63–70.
Mizoguchi, R., Sunagawa, E., Kozaki, K. and Kitamura, Y. (2007). A Model of Roles within an Ontology Development Tool:
Hozo, Applied Ontology 2(2), 159–179.
Nishimura, S., Kitamura, Y., Sasajima, M. and Mizoguchi, R. (2014). Systematic Description of Nursing Actions Based on Goal
Realization Model, In Proceednigs of the 15th European Conference on Knowledge Management (ECKM2014), Santarém,
Portugal, September 4–5, 2014, 730–739.
Peirce, C. S. (1977). Semiotic and Significs: The Correspondence between Charles S. Peirce and Victoria Lady Welby, edited by
Charles S. Hardwick, Bloomington: Indiana University Press.
Rovetto, R. J. and Mizoguchi, R. (2015). Causality and the ontology of disease, Applied Ontology, 10(2), 79–105.
Sasajima, M., Kitamura, Y., Naganuma, T., Fujii, K., Kurakake, S. and Mizoguchi, R. (2008). Obstacles Reveal the Needs ofMobile Internet Services - OOPS: Ontology-based Obstacles, Prevention and Solution Modeling Framework. Journal of Web
Engineering, 7(2), 133–157.
Scheuermann, R. H., Ceuster, W. and Smith, B. (2009). Towards an Ontological Treatment of Disease and Diagnosis. In Summit
on Translational Bioinformatics, 116–120.
Smith, B. and Ceusters, W. (2010). Ontological realism: A methodology for coordinated evolution of scientific ontologies, Applied Ontology, 5(3-4), 139–188.
Steven, S. S. (1946). On the Theory of Scales of Measurement. Science, 103(2684), 677–680.
Sumita, K., Kitamura, Y., Sasajima, M. and Mizoguchi, R. (2012). Are Services Functions? In Proceedings of the Third International Conference on Exploring Services Science (IESS2012), Geneva, Switzerland, February 15–17, 2012, 58–72.
Toyoshima, F., Mizoguchi, R. and Ikeda, M. (2017). Causation and the River Flow Model of Diseases. In Proceedings of
the 8th International Conference on Biomedical Ontology (ICBO2017), Newcastle upon Tyne, UK, 13–15 September,2017.Accepted.
Tsang, E. P. K. (1987). Time Structures for AI. In Proceedings of 10th International Joint Conference on AI (IJCAI), 456–461.
Yamagata, Y., Kozaki, K., Imai, T., Ohe, K. and Mizoguchi, R. (2014). An ontological modeling approach for abnormal statesand its application in the medical domain, Journal of biomedical semantics 5(1), 1–14.